1GM6

3-D STRUCTURE OF A SALIVARY LIPOCALIN FROM BOAR

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.254 

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This is version 1.2 of the entry. See complete history. 


Literature

Boar Salivary Lipocalin. Three-Dimensional X-Ray Structure and Androsterol/Androstenone Docking Simulations.

Spinelli, S., Vincent, F., Pelosi, P., Tegoni, M., Cambillau, C.

(2002) Eur J Biochem 269: 2449

  • DOI: 10.1046/j.1432-1033.2002.02901.x
  • Primary Citation of Related Structures:  
    1GM6

  • PubMed Abstract: 

    • The X-ray structure of variant A of authentic boar salivary lipocalin (SAL), a pheromone-binding protein specifically expressed in the submaxillary glands of the boar, has been solved and refined at 2.1 A resolution. The structure displays a classical lipocalin fold with a nine-stranded sandwiched beta barrel and an alpha helix ...

    The X-ray structure of variant A of authentic boar salivary lipocalin (SAL), a pheromone-binding protein specifically expressed in the submaxillary glands of the boar, has been solved and refined at 2.1 A resolution. The structure displays a classical lipocalin fold with a nine-stranded sandwiched beta barrel and an alpha helix. A putative glycosylation site, at position 53, has been found to carry a GlcNAc sugar residue. In contrast with what was expected on the basis of mass spectroscopy reports, the internal cavity was found to be devoid of bound pheromonal compound (androstenone or androstenol). Instead, a small electron density volume could be satisfied by a glycerol molecule, a component of the cryoprotecting liquor. The internal cavity was revealed to be very small for steroid compound accommodation. Therefore, docking and molecular dynamics experiments were performed with both pheromonal compounds. These simulations clearly demonstrate a volume increase of the cavity upon steroid binding and the adaptation of the amino-acid side chains to the steroid molecules. This explains the higher affinity of SAL for both steroid molecules compared to other smaller molecules, although no specific interaction is established with either compound.

    Organizational Affiliation: 

    Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités Aix-Marseille I & II, France.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SALIVARY LIPOCALINA175Sus scrofaMutation(s): 0 
Gene Names: SAL1
UniProt
Find proteins for P81608 (Sus scrofa)
Explore P81608 
Go to UniProtKB:  P81608
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP81608
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
D [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
CD
Query on CD
Download Ideal Coordinates CCD File 
B [auth A]CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.254 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.112α = 90
b = 70.112β = 90
c = 71.75γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-05-30
    Type: Initial release
  • Version 1.1: 2011-09-07
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary